Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments
Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of...
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MDPI AG
2020-12-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/12/1480 |
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| author | Adam Abied Lei Xu Bahlibi W. Sahlu Feng Xing Abulgasim Ahbara Yabin Pu Jiang Lin Haile Berihulay Rabiul Islam Xiaohong He Joram M. Mwacharo Qianjun Zhao Yuehui Ma |
| author_facet | Adam Abied Lei Xu Bahlibi W. Sahlu Feng Xing Abulgasim Ahbara Yabin Pu Jiang Lin Haile Berihulay Rabiul Islam Xiaohong He Joram M. Mwacharo Qianjun Zhao Yuehui Ma |
| author_sort | Adam Abied |
| collection | DOAJ |
| description | Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (<i>5S_rRNA</i>), the innate and adaptive immune response (<i>HERC2</i> and <i>CYFIP1</i>), digestion and metabolism (<i>CENPJ</i>), growth (SPP1), body size and developments (<i>GJB2</i> and <i>GJA3</i>). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds. |
| first_indexed | 2024-03-10T14:12:18Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T14:12:18Z |
| publishDate | 2020-12-01 |
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| series | Genes |
| spelling | doaj.art-0564ea41cfc94fda99f6e40c337a31242023-11-21T00:03:35ZengMDPI AGGenes2073-44252020-12-011112148010.3390/genes11121480Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different EnvironmentsAdam Abied0Lei Xu1Bahlibi W. Sahlu2Feng Xing3Abulgasim Ahbara4Yabin Pu5Jiang Lin6Haile Berihulay7Rabiul Islam8Xiaohong He9Joram M. Mwacharo10Qianjun Zhao11Yuehui Ma12The Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaInstitute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaInstitute of Animal Science (IAS), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaCollege of Animal Science, Tarim University (TU), Alar 843300, Xinjiang, ChinaSchool of Life Sciences, University of Nottingham, Nottingham NG7 2RD, UKThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaInternational Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa 1108-2010, EthiopiaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaThe Key Laboratory for Farm Animal Genetic Resources and Utilization, Ministry of Agriculture and Rural Affairs, Institute of Animal Science Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, ChinaHomozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (<i>5S_rRNA</i>), the innate and adaptive immune response (<i>HERC2</i> and <i>CYFIP1</i>), digestion and metabolism (<i>CENPJ</i>), growth (SPP1), body size and developments (<i>GJB2</i> and <i>GJA3</i>). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds.https://www.mdpi.com/2073-4425/11/12/1480high-densitySNPssheepinbreedingminor allele frequency |
| spellingShingle | Adam Abied Lei Xu Bahlibi W. Sahlu Feng Xing Abulgasim Ahbara Yabin Pu Jiang Lin Haile Berihulay Rabiul Islam Xiaohong He Joram M. Mwacharo Qianjun Zhao Yuehui Ma Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments Genes high-density SNPs sheep inbreeding minor allele frequency |
| title | Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments |
| title_full | Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments |
| title_fullStr | Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments |
| title_full_unstemmed | Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments |
| title_short | Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments |
| title_sort | genome wide analysis revealed homozygosity and demographic history of five chinese sheep breeds adapted to different environments |
| topic | high-density SNPs sheep inbreeding minor allele frequency |
| url | https://www.mdpi.com/2073-4425/11/12/1480 |
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